IMPORTANT! VectorBase to merge with EupathDB

Dear VectorBasers,

In July 2004 the Bioinformatics Resource Centers (BRCs) were started and funded by the National Institute of Allergy and Infectious Diseases (NIAID) within the US National Institutes of Health (NIH). In the beginning, there were eight BRCs (Greene et al. 2007), and today there are five covering: influenza virus (IRD), all other viruses (ViPR), bacteria (PATRIC), eukaryotic pathogens and fungi (EuPathDB) and invertebrate vectors of human pathogens (VectorBase). The BRC funding cycles span five years and the current contract will end September 2019. For the fourth round of BRC funding, NIAID-NIH will further consolidate the BRCs by requesting applications for only two contracts, one that covers bacteria and viruses and the other to cover protozoa, fungi and invertebrate vectors of human pathogens. On January 10, 2019, VectorBase and EuPathDB submitted a joint contract proposal to NIAID-NIH. Though we cannot guarantee to be the recipient of the next five years' funding, it is in the community's interest that we make plans assuming we will be successful. What does this mean for you?

The expectation is to provide a better service to all user communities, to improve capabilities to query across a wider taxonomic range of organisms, and to develop systems biology approaches to scientific problems. In the case of the vector community, this could allow the hosting and integration of data sets from experiments in which the vector and parasite/pathogen genes differential expression is been measured simultaneously, or the study of microbiomes associated with vectors or identification of data from a single geographic location that includes both vector and parasite phenotypes. The combined BRC will leverage the strengths of both VectorBase and EuPathDB, including their best tools and resources as well as a merger of their staff and outreach personnel, which will result in improved service to both the vector and parasite communities.

If a BRC contract is awarded to support an integrated VectorBase / EuPathDB resource, the vector community can anticipate the following.

  1. The current VectorBase website will continue to be available and functional until September 2019. After that time a static version of the site will be available until the initial systems integration with EuPathDB is completed in early 2020. If another entity is awarded the contract, it is likely that a similar time frame will result.
  2. VectorBase will continue normal releases until August 2019 after which we will temporarily halt releases. The last release of the current BRC contract will be August 2019, and this release will continue to be available until the new merged BRC or some other entity begins operating.
  3. We strongly encourage all our community members that are considering submitting new data to do so at your earliest convenience. We will continue to receive new data and manual annotations via Apollo throughout the merger, but it may not be possible to process received data into the public database releases before the merger process is completed in March 2020. To guarantee inclusion of a submitted data set from a source other than Apollo into VectorBase prior to September 2019 we will need to have received the submission by March 2019 - this will allow us time to complete the work for the June and August releases.
  4. Data release is expected to resume again six months after the merger (May 2020).
  5. All data sets will be affected by the submission freeze in March 2019, including but not limited to: reference and variant genome sequence, structural annotations (e.g. gene models, protein domains), functional annotations, and phenotypic and population data for traits such as insecticide resistance. We will also stop importing data from external databases and generating primary data after June 2019. For example, we will not recalculate homology relationships i.e., paralogs and orthologs, the effect of sequence variations on protein coding sequences, and the mapping of array probes to updated gene models.
  6. Even though all data will be kept, some of the VectorBase tools will be lost as we migrate to the new BRC. We anticipate the functionality of most of these tools will be replicated by other systems on the new website, and we will provide the full list of resources to be lost and their proposed replacements in a timely manner. The BioMart, compara orthology database, and Sample and GenoType Explorer applications will not be supported in the new BRC, but our colleagues at Ensembl metazoa will continue to offer support of VectorBase organisms via the Ensembl genome browser, BioMart, and compara systems after August 2019.
  7. We will post updates regularly on our News page and Release notes, as well as in our social media groups. We might send emails too, but will try to keep these to a minimum.
  8. If you have recommendations for the possible new name and logo with which the newly merged vector, eukaryotic and fungal website resource could be identified please provide your feedback in this Google form.

As always, please feel free to email us at info@vectorbase.org if you have any concerns about how this new change may affect your previously submitted data, current or future projects. We are committed to supporting you in your work, and will do all we can to make this transition process as simple and painless as possible. Once we hear the outcome of our application to NIAID-NIH we will inform you, our user community, of the outcome.

It has been our pleasure to work with you, and we look forward to continuing our close relationship in a new merged BRC. With huge thanks, appreciation and deep gratitude to you all,

The VectorBase team

Reference

Greene, J. M., Collins, F., Lefkowitz, E. J., Roos, D., Scheuermann, R. H., Sobral, B., Stevens, R., White, O., … Di Francesco, V. (2007). National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infection and immunity, 75(7), 3212-9.